The DOI matches its Crossref record; 34 of the 36 references it cites were found in a registry or an index.
Accurate whole human genome sequencing using reversible terminator chemistry
Open accessAbstract
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400–800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30× average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications. The power of the latest massively parallel synthetic DNA sequencing technologies is demonstrated in two major collaborations that shed light on the nature of genomic variation with ethnicity. The first describes the genomic characterization of an individual from the Yoruba ethnic group of west Africa. The second reports a personal genome of a Han Chinese, the group comprising 30% of the world's population. These new resources can now be used in conjunction with the Venter, Watson and NIH reference sequences. A separate study looked at genetic ethnicity on the continental scale, based on data from 1,387 individuals from more than 30 European countries. Overall there was little genetic variation between countries, but the differences that do exist correspond closely to the geographic map. Statistical analysis of the genome data places 50% of the individuals within 310 km of their reported origin. As well as its relevance for testing genetic ancestry, this work has implications for evaluating genome-wide association studies that link genes with diseases.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Over the last two years, with the further confirmation that the relatively short reads can be effectively assembled [15], especially with the great advantage of paired-end sequencing [54], the Illumina transcriptome or whole genome de novo sequencing and assembly have been successfully used for model [12,16,55-58]and non-model organisms [25-27,59].”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [15]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The newly developed high throughput sequencing technology, i.e. Next Generation Sequencing (NGS), including the Roche/454 Genome Sequencer FLX Instrument, the ABI SOLiD System, and the Illumina Genome Analyser, is a powerful and cost-efficient tool for advanced research in many areas, including re-sequencing, microRNA expression profiling, DNA methylation, especially de novo transcriptome”
From De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) (2010) · cites this paper as [15]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Self-citationA haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Self-citationFinishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Flagged first, then by citations
2 of the 36 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 401–500 of 1,010
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Lam, H. Y. K., Mu, X. J., Stütz, A. M., Andrea Tanzer, A., Cayting, P. D., Snyder, M. P., Kim, P. M., Korbel, J. O., & Gerstein, M. (2009) · Nature Biotechnology · doi:10.1038/nbt.1600 · Cited by 193
Holtgrewe, M. (2010) · Europe PMC (PubMed Central) · doi:10.17169/refubium-22374 · Cited by 191
The neandertal genome and ancient DNA authenticity
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190
Impact of next generation sequencing techniques in food microbiology.
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R., & Delgado, S. (2014) · Current Genomics · doi:10.2174/1389202915666140616233211 · Cited by 188
SNP discovery in the bovine milk transcriptome using RNA-Seq technology
Cánovas, Á., Rincón, G., Islas‐Trejo, A., Wickramasinghe, S., & Medrano, J. F. F. (2010) · Mammalian Genome · doi:10.1007/s00335-010-9297-z · Cited by 188
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome
Miller, A. R., Hawkins, N. A., McCollom, C. E., & Kearney, J. A. (2013) · Genes Brain & Behavior · doi:10.1111/gbb.12099 · Cited by 185
The impact of next-generation sequencing technologies on HLA research
Hosomichi, K., Shiina, T., Tajima, A., & Inoue, I. (2015) · Journal of Human Genetics · doi:10.1038/jhg.2015.102 · Cited by 193
Targeted exome sequencing of suspected mitochondrial disorders
Lieber, D. S., Calvo, S. E., Shanahan, K., Slate, N. G., Liu, S., Hershman, S. G., Gold, N. B., Chapman, B., Thorburn, D. R., Berry, G. T., et al. (2013) · Neurology · doi:10.1212/wnl.0b013e3182918c40 · Cited by 188
Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches
Chandran, H., Meena, M., & Sharma, K. (2020) · Frontiers in Environmental Chemistry · doi:10.3389/fenvc.2020.570326 · Cited by 197
Genome-wide association studies in mice
Flint, J., & Eskin, E. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3335 · Cited by 191
A statistical method for the detection of variants from next-generation resequencing of DNA pools
Bansal, V. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq214 · Cited by 188
Comparative Mechanistic Studies of Brilacidin, Daptomycin, and the Antimicrobial Peptide LL16
Mensa, B., Howell, G. L., Scott, R. W., & DeGrado, W. F. (2014) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02955-14 · Cited by 186
Whole-genome CNV analysis: advances in computational approaches
Pirooznia, M., Goes, F. S., & Zandi, P. P. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00138 · Cited by 202
Evolutionary History of the Clostridium difficile Pathogenicity Locus
Dingle, K. E., Elliott, B., Robinson, E., Griffiths, D. J., Eyre, D. W., Stoesser, N. E., Vaughan, A., Golubchik, T., Fawley, W. N., Wilcox, M. H., et al. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt204 · Cited by 185
Deep Whole-Genome Sequencing of 100 Southeast Asian Malays
Wong, L.-P., Ong, R. T., Poh, W.-T., Liu, X., Chen, P., Li, R., Lam, K., Pillai, N. E., Sim, K. S., Xu, H., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.12.005 · Cited by 182
Self-citationWhole genome sequencing in clinical practice
Bagger, F. O., Borgwardt, L. G., Jespersen, A. S., Hansen, A. R., Bertelsen, B., Kodama, M., & Nielsen, F. C. (2024) · BMC Medical Genomics · doi:10.1186/s12920-024-01795-w · Cited by 210
The clinical context of copy number variation in the human genome
Lee, C., & Scherer, S. W. (2010) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399410001390 · Cited by 188
Cosentino, S., Larsen, M. V., Aarestrup, F. M., & Lund, O. (2013) · PLoS ONE · doi:10.1371/annotation/b84e1af7-c127-45c3-be22-76abd977600f · Cited by 184
Stanton‐Geddes, J., Paape, T. D., Epstein, B., Briskine, R. V., Yoder, J. B., Mudge, J., Bharti, A. K., Farmer, A. D., Zhou, P., Denny, R. L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065688 · Cited by 186
Visualizing biologically active small molecules in cells using click chemistry
Cañeque, T., Müller, S., & Rodriguez, R. (2018) · Nature Reviews Chemistry · doi:10.1038/s41570-018-0030-x · Cited by 185
Pendleton, A. L., Shen, F., Taravella, A. M., Emery, S., Veeramah, K. R., Boyko, A. R., & Kidd, J. M. (2018) · BMC Biology · doi:10.1186/s12915-018-0535-2 · Cited by 156
The pursuit of genome-wide association studies: where are we now?
Ku, C., Loy, E. Y., Yudi Pawitan, Y., & Chia, K. S. (2010) · Journal of Human Genetics · doi:10.1038/jhg.2010.19 · Cited by 184
The genomic landscape shaped by selection on transposable elements across 18 mouse strains
Nellåker, C., Keane, T., Yalcin, B., Wong, K., Agam, A., Belgard, T. G., Flint, J., Adams, D. J., Frankel, W. N., & Ponting, C. P. (2012) · Genome biology · doi:10.1186/gb-2012-13-6-r45 · Cited by 177
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
MacCallum, I., Przybylski, D., Gnerre, S., Burton, J. N., Shlyakhter, I. A., Gnirke, A., Malek, J. A., McKernan, K. J., Ranade, S., Shea, T., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-10-r103 · Cited by 180
Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery
Flynn, C. R., Albaugh, V. L., Cai, S. B., Cheung‐Flynn, J., Williams, P. E., Brucker, R. M., Bordenstein, S. R., Guo, Y. P., Wasserman, D. H., & Abumrad, N. N. (2015) · Nature Communications · doi:10.1038/ncomms8715 · Cited by 185
Hodges, E. C., Rooks, M. G., Xuan, Z., Bhattacharjee, A., Gordon, D. B., Brizuela, L., McCombie, W. R., & Hannon, G. J. (2009) · Nature Protocols · doi:10.1038/nprot.2009.68 · Cited by 174
Talkowski, M. E., Ernst, C., Heilbut, A. M., Chiang, C., Hanscom, C., Lindgren, A. M., Kirby, A. W., Liu, S., Muddukrishna, B., Ohsumi, T. K., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.013 · Cited by 177
Genome-Wide Translational Profiling by Ribosome Footprinting
Ingolia, N. T. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70006-9 · Cited by 177
Tucker, E. J., Hershman, S. G., Köhrer, C., Belcher-Timme, C. A., Patel, J., Goldberger, O., Christodoulou, J., Silberstein, J. M., McKenzie, M., Ryan, M. T., et al. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.07.010 · Cited by 176
Bleidorn, C. (2015) · Systematics and Biodiversity · doi:10.1080/14772000.2015.1099575 · Cited by 183
Detecting copy number variation with mated short readsPreprint
Medvedev, P., Fiume, M., Dzamba, M., Smith, T. P. L., & Brudno, M. (2010) · Genome Research · doi:10.1101/gr.106344.110 · Cited by 178
Ho, P., Lo, W. U., Yeung, M. K., Lin, C. H., Chow, K. H., Ang, I. L., Tong, A. H. Y., Bao, J. Y. J., Lok, S., & Lo, J. Y. C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017989 · Cited by 175
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors
Jones, S. J. M., Laskin, J. J., Li, Y. Y., Griffith, O. L., An, J., Bilenky, M., Butterfield, Y. S. N., Cezard, T., Chuah, E., Corbett, R., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-8-r82 · Cited by 174
Zheng, W., Wang, Z., Collins, J. E., Andrews, R., Stemple, D. L., & Gong, Z. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024019 · Cited by 172
Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
Guo, Y., Dai, Y., Yu, H., Zhao, S., Samuels, D. C., & Shyr, Y. (2017) · Genomics · doi:10.1016/j.ygeno.2017.01.005 · Cited by 172
Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection
Li, S., Zhang, X., Sun, Z., Li, F., & Xiang, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058627 · Cited by 173
Meta'omic Analytic Techniques for Studying the Intestinal Microbiome
Morgan, X. C., & Huttenhower, C. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.049 · Cited by 181
DNA-based memory devices for recording cellular events
Sheth, R. U., & Wang, H. H. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0052-8 · Cited by 179
Yin, X., Kim, K.-W., Suetsugu, H., Bang, S., Wen, L., Koido, M., Ha, E., Liu, L., Sakamoto, Y., Jo, S., et al. (2020) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2020-219209 · Cited by 175
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Self-citationA network medicine approach to human disease
Zanzoni, A., Soler‐López, M., & Aloy, P. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.03.001 · Cited by 172
Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade
Xi, Z., Wang, Y., Bradley, R. K., Sugumaran, M., Marx, C. J., Rest, J. S., & Davis, C. “. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003265 · Cited by 170
Cryptosporidium: parasite and disease
Cacciò, S. M., & Widmer, G. (2013) · Springer eBooks · doi:10.1007/978-3-7091-1562-6 · Cited by 170
Unlocking short read sequencing for metagenomics
Rodrigue, S., Materna, A. C., Timberlake, S. C., Blackburn, M. C., Malmstrom, R. R., Alm, E. J., & Chisholm, S. W. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011840 · Cited by 168
Rafaelsen, S., Ræder, H., Fagerheim, A. K., Knappskog, P. M., Carpenter, T. O., Johansson, S., & Bjerknes, R. (2013) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.1850 · Cited by 169
Lang, D., Zhang, S., Ren, P., Liang, F., Sun, Z., Meng, G., Tan, Y., Hu, J., Lai, Q., Lai, Q., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa123 · Cited by 177
Copy number variation in the bovine genome
Fadista, J., Thomsen, B., Holm, L., & Bendixen, C. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-284 · Cited by 171
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
Mukherjee, S., Huntemann, M., Ivanova, N., Kyrpides, N. C., & Pati, A. (2015) · Standards in Genomic Sciences · doi:10.1186/1944-3277-10-18 · Cited by 166
Polymorphic Cis- and Trans-Regulation of Human Gene Expression
Cheung, V. G., Nayak, R. R., Wang, I. X., Elwyn, S., Cousins, S. M., Morley, M. P., & Spielman, R. S. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000480 · Cited by 168
Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects
Barbosa, C., Trebosc, V., Kemmer, C., Rosenstiel, P. C., Beardmore, R., Schulenburg, H., & Jansen, G. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx158 · Cited by 154
Using ERDS to Infer Copy-Number Variants in High-Coverage Genomes
Zhu, M., Need, A. C., Han, Y., Ge, D., Maia, J. M., Zhu, Q., Heinzen, E. L., Cirulli, E. T., Pelak, K., He, M., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.07.004 · Cited by 168
GemSIM: general, error-model based simulator of next-generation sequencing data
McElroy, K., Luciani, F., & Thomas, T. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-74 · Cited by 165
Krishna, A., Biryukov, M., Trefois, C., Antony, P. M. A., Hussong, R., Lin, J., Heinäniemi, M., Glusman, G., Köglsberger, S., Boyd, O., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-1154 · Cited by 174
Comprehensive comparison of three commercial human whole-exome capture platforms
Asan, Xu, Y., Jiang, H., Tyler‐Smith, C., Xue, Y., Jiang, T., Wang, J., Wu, M., Liu, X., Tian, G., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r95 · Cited by 165
Self-citationStructural Insights into the Processing of Nucleobase-Modified Nucleotides by DNA Polymerases
Hottin, A., & Marx, A. (2016) · Accounts of Chemical Research · doi:10.1021/acs.accounts.5b00544 · Cited by 164
H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in AfricaPreprint
Mulder, N., Adebiyi, E. F., Alami, R., Benkahla, A., Brandful, J., Doumbia, S., Everett, D., Fadlelmola, F. M., Gaboun, F., Gaseitsiwe, S., et al. (2015) · Genome Research · doi:10.1101/gr.196295.115 · Cited by 172
Abel, H., & Duncavage, E. J. (2013) · Cancer Genetics · doi:10.1016/j.cancergen.2013.11.002 · Cited by 164
Expression in Aneuploid Drosophila S2 Cells
Zhang, Y., Malone, J. H., Powell, S., Periwal, V., Spana, E. P., MacAlpine, D. M., & Oliver, B. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000320 · Cited by 161
Genomic-scale capture and sequencing of endogenous DNA from feces
Perry, G. H., Marioni, J. C., Melsted, P., & Gilad, Y. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04888.x · Cited by 165
Addressing challenges in the production and analysis of illumina sequencing data
Kircher, M., Heyn, P. C., & Kelso, J. F. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-382 · Cited by 172
A method for counting PCR template molecules with application to next-generation sequencing
Casbon, J. A., Osborne, R. J., Brenner, S., & Lichtenstein, C. P. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr217 · Cited by 158
DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysisPreprint
Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M. G., & Hannon, G. J. (2009) · Genome Research · doi:10.1101/gr.092957.109 · Cited by 165
Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain
Fu, X., Sun, L., Dong, R., Chen, J. Y., Silakit, R., Condon, L. F., Lin, Y., Lin, S., Palmiter, R. D., & Gu, L. (2022) · Cell · doi:10.1016/j.cell.2022.10.021 · Cited by 161
Base-calling for next-generation sequencing platforms
Ledergerber, C., & Dessimoz, C. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbq077 · Cited by 161
Detecting false-positive signals in exome sequencing
Fajardo, K. V. F., Adams, D. R., Program, N. C. S., Mason, C. E., Sincan, M., Tifft, C. J., Toro, C., Boerkoel, C. F., Gahl, W. A., & Markello, T. C. (2012) · Human Mutation · doi:10.1002/humu.22033 · Cited by 158
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Sboner, A., Habegger, L., Pflueger, D., Terry, S., Chen, D. Z., Rozowsky, J. S., Tewari, A. K., Kitabayashi, N., Moss, B. J., Chee, M. S., et al. (2010) · Genome biology · doi:10.1186/gb-2010-11-10-r104 · Cited by 158
Kleiner, R. E., Dumelin, C. E., Tiu, G. C., Sakurai, K., & Liu, D. R. (2010) · Journal of the American Chemical Society · doi:10.1021/ja104903x · Cited by 158
Zhao, Y., Zuo, X., Li, Q., Chen, F., Chen, Y.-R., Deng, J., Han, D., Hao, C., Huang, F., Huang, Y., et al. (2020) · Science China Chemistry · doi:10.1007/s11426-020-9864-7 · Cited by 167
Self-citationChallenges of sequencing human genomes
Koboldt, D. C., Ding, L., Mardis, E. R., & Wilson, R. K. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq016 · Cited by 161
A Wide Extent of Inter-Strain Diversity in Virulent and Vaccine Strains of Alphaherpesviruses
SZPARA, M. L., Tafuri, Y. R., Parsons, L. R., Shamim, S. R., Verstrepen, K. J., Legendre, M., & Enquist, L. W. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002282 · Cited by 157
RazerS--fast read mapping with sensitivity control.Preprint
Weese, D., Emde, A., Rausch, T., Döring, A., & Reinert, K. (2009) · Genome Research · doi:10.1101/gr.088823.108 · Cited by 178
Chung, H.-Y., Wickel, J., Hahn, N., Mein, N., Schwarzbrunn, M., Koch, P., Ceanga, M., Haselmann, H., Baade-Büttner, C., von Stackelberg, N., et al. (2023) · Science Advances · doi:10.1126/sciadv.abq7806 · Cited by 156
Improved Protocols for the Illumina Genome Analyzer Sequencing System
Quail, M. A., Swerdlow, H., & Turner, D. (2009) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1802s62 · Cited by 156
Self-citationLinking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, M., Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarević, D., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1470 · Cited by 154
The Characterization of Twenty Sequenced Human Genomes
Pelak, K., Shianna, K. V., Ge, D., Maia, J. M., Zhu, M., Smith, J. P., Cirulli, E. T., Fellay, J., Dickson, S. P., Gumbs, C. E., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001111 · Cited by 159
Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls
Horak, P., Fröhling, S., & Glimm, H. (2016) · ESMO Open · doi:10.1136/esmoopen-2016-000094 · Cited by 162
Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches
Khodakov, D. A., Wang, C., & Zhang, D. Y. (2016) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2016.04.005 · Cited by 159
Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics
Gibbons, J. G., Janson, E. M., Hittinger, C. T., Johnston, M., Abbot, P., & Rokas, A. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp188 · Cited by 159
Assessing structural variation in a personal genome—towards a human reference diploid genome
English, A. C., Salerno, W. J., Hampton, O. A., Gonzaga-Jauregui, C. G., Ambreth, S., Ritter, D., Beck, C. R., Davis, C., Dahdouli, M., Ma, S., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1479-3 · Cited by 152
Self-citationOikonomopoulos, S., Wang, Y. C., Djambazian, H. H. V., Badescu, D., & Ragoussis, J. (2016) · Scientific Reports · doi:10.1038/srep31602 · Cited by 153
Applications and analysis of targeted genomic sequencing in cancer studies
Bewicke‐Copley, F., Kumar, E. A., Palladino, G., Korfi, K., & Wang, J. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.10.004 · Cited by 164
Self-citationGreil, J., Rausch, T., Giese, T., Bandapalli, O. R., Daniel, V., Bekeredjian‐Ding, I., Stütz, A. M., Drees, C., Roth, S., Ruland, J., et al. (2013) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.02.012 · Cited by 152
Young, N. D., Campbell, B. E., Hall, R. S., Jex, A. R., Cantacessi, C., Laha, T., Sohn, W., Sripa, B., Loukas, A. C., Brindley, P. J., et al. (2010) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0000719 · Cited by 151
Characterization of missing human genome sequences and copy-number polymorphic insertions
Kidd, J. M., Sampas, N., Antonacci, F., Graves, T., Fulton, R. S., Hayden, H. S., Alkan, C., Malig, M., Ventura, M., Giannuzzi, G., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1451 · Cited by 150
Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens
Rowe, K. C., Singhal, S., MacManes, M. D., Ayroles, J. F., Morelli, T. L., Rubidge, E. M., Bi, K., & Moritz, C. C. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.03052.x · Cited by 151
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Baid, G., Cook, D. E., Shafin, K., Yun, T., Llinares-López, F., Berthet, Q., Belyaeva, A., Töpfer, A., Wenger, A. M., Rowell, W. J., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01435-7 · Cited by 155
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
Deschamps, S., & Campbell, M. A. (2009) · Molecular Breeding · doi:10.1007/s11032-009-9357-9 · Cited by 153
Niemann, S., Köser, C. U., Gagneux, S., Plinke, C., Homolka, S., Bignell, H., Carter, R. J., Cheetham, R. K., Cox, A., Gormley, N. A., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007407 · Cited by 149
Self-citationNext-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research
Hodkinson, B. P., & Grice, E. A. (2014) · Advances in Wound Care · doi:10.1089/wound.2014.0542 · Cited by 155
Baumgart, M., Priebe, S., Groth, M., Hartmann, N., Menzel, U., Pandolfini, L., Koch, P., Felder, M., Ristow, M., Englert, C., et al. (2016) · Cell Systems · doi:10.1016/j.cels.2016.01.014 · Cited by 150
Fuller, C. W., Kumar, S., Porel, M., Chien, M., Bibillo, A., Stranges, P. B., Dorwart, M. R., Tao, C., Li, Z., Guo, W., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601782113 · Cited by 149
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
den Berge, K. V., Hembach, K., Soneson, C., Tiberi, S., Clement, L., Love, M. I., Patro, R., & Robinson, M. D. (2019) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-072018-021255 · Cited by 153
Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects
Ballard, D., Winkler-Galicki, J., & Wesoły, J. (2020) · International Journal of Legal Medicine · doi:10.1007/s00414-020-02294-0 · Cited by 148
Manual of Aquatic Viral Ecology
Wilhelm, S., Weinbauer, M., & Suttle, C. (2010) · doi:10.4319/mave.2010.978-0-9845591-0-7 · Cited by 159
High Persister Mutants in Mycobacterium tuberculosis
Torrey, H. L., Keren, I., Via, L. E., Lee, J. S., & Lewis, K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155127 · Cited by 147
Genomics of wood-degrading fungi
Ohm, R. A., Riley, R. W., Salamov, A. A., Min, B., Choi, I., & Grigoriev, I. V. (2014) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2014.05.001 · Cited by 146
Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics
Dorey, A., & Howorka, S. (2024) · Nature Chemistry · doi:10.1038/s41557-023-01322-x · Cited by 155
RNA-sequence analysis of human B-cells
Toung, J. M., Morley, M., Li, M., & Cheung, V. G. (2011) · Genome Research · doi:10.1101/gr.116335.110 · Cited by 142
Nucleobase modification as redox DNA labelling for electrochemical detection
Hocek, M., & Fojta, M. (2011) · Chemical Society Reviews · doi:10.1039/c1cs15049a · Cited by 148
Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data
Auburn, S., Campino, S. G., Miotto, O., DJIMDÉ, A. A., Zongo, I., Manske, M., Maslen, G. L., Mangano, V. D., Alcock, D., MacInnis, B. L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032891 · Cited by 145
Metadata
- Authors
- Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., Boutell, J. M., Bryant, J., Carter, R. J., Keira Cheetham, R., Cox, A. J., Ellis, D. J., Flatbush, M. R., Gormley, N. A., Humphray, S. J., Irving, L. J., Karbelashvili, M. S., Kirk, S. M., Li, H., Liu, X., Maisinger, K. S., Murray, L. J., Obradovic, B., Ost, T., Parkinson, M. L., Pratt, M. R., Rasolonjatovo, I. M. J., Reed, M. T., Rigatti, R., Rodighiero, C., Ross, M. T., Sabot, A., Sankar, S. V., Scally, A., Schroth, G. P., Smith, M. E., Smith, V. P., Spiridou, A., Torrance, P. E., Tzonev, S. S., Vermaas, E. H., Walter, K., Wu, X., Zhang, L., Alam, M. D., Anastasi, C., Aniebo, I. C., Bailey, D. M. D., Bancarz, I. R., Banerjee, S., Barbour, S. G., Baybayan, P. A., Benoit, V. A., Benson, K. F., Bevis, C., Black, P. J., Boodhun, A., Brennan, J. S., Bridgham, J. A., Brown, R. C., Brown, A. A., Buermann, D. H., Bundu, A. A., Burrows, J. C., Carter, N. P., Castillo, N., Chiara E. Catenazzi, M., Chang, S., Neil Cooley, R., Crake, N. R., Dada, O. O., Diakoumakos, K. D., Dominguez-Fernandez, B., Earnshaw, D. J., Egbujor, U. C., Elmore, D. W., Etchin, S. S., Ewan, M. R., Fedurco, M., Fraser, L. J., Fuentes Fajardo, K. V., Scott Furey, W., George, D., Gietzen, K. J., Goddard, C. P., Golda, G. S., Granieri, P. A., Green, D. E., Gustafson, D. L., Hansen, N. F., Harnish, K., Haudenschild, C. D., Heyer, N. I., Hims, M. M., Ho, J. T., Horgan, A. M., Hoschler, K., Hurwitz, S., Ivanov, D. V., Johnson, M. Q., James, T., Huw Jones, T. A., Kang, G.-D., Kerelska, T. H., Kersey, A. D., Khrebtukova, I., Kindwall, A. P., Kingsbury, Z., Kokko-Gonzales, P. I., Kumar, A., Laurent, M. A., Lawley, C. T., Lee, S. E., Lee, X., Liao, A. K., Loch, J. A., Lok, M., Luo, S., Mammen, R. M., Martin, J. W., McCauley, P. G., McNitt, P., Mehta, P., Moon, K. W., Mullens, J. W., Newington, T., Ning, Z., Ling Ng, B., Novo, S. M., O’Neill, M. J., Osborne, M. A., Osnowski, A., Ostadan, O., Paraschos, L. L., Pickering, L., Pike, A. C., Pike, A. C., Chris Pinkard, D., Pliskin, D. P., Podhasky, J., Quijano, V. J., Raczy, C., Rae, V. H., Rawlings, S. R., Chiva Rodriguez, A., Roe, P. M., Rogers, J., Rogert Bacigalupo, M. C., Romanov, N., Romieu, A., Roth, R. K., Rourke, N. J., Ruediger, S. T., Rusman, E., Sanches-Kuiper, R. M., Schenker, M. R., Seoane, J. M., Shaw, R. J., Shiver, M. K., Short, S. W., Sizto, N. L., Sluis, J. P., Smith, M. A., Ernest Sohna Sohna, J., Spence, E. J., Stevens, K., Sutton, N., Szajkowski, L., Tregidgo, C. L., Turcatti, G., vandeVondele, S., Verhovsky, Y., Virk, S. M., Wakelin, S., Walcott, G. C., Wang, J., Worsley, G. J., Yan, J., Yau, L., Zuerlein, M., Rogers, J., Mullikin, J. C., Hurles, M. E., McCooke, N. J., West, J. S., Oaks, F. L., Lundberg, P. L., Klenerman, D., Durbin, R., & Smith, A. J.
- Affiliations
- Illumina (United Kingdom) (GB)
- University of Cambridge (GB)
- Wellcome Sanger Institute (GB)
- Illumina (United States) (US)
- National Institutes of Health (US)
- Corresponding author
- Bentley, David R.
- ORCID
- Balasubramanian, Shankar
- Swerdlow, Harold P.
- Hall, Kevin P.
- Humphray, Sean J.
- Li, Heng
- Liu, Xiaohai
- Ross, Mark T.
- Scally, Aylwyn
- Schroth, Gary P.
- Spiridou, Anastassia
- Walter, Klaudia
- Wu, Xiaolin
- Bailey, David M. D.
- Brown, Andrew A.
- Fraser, Louise J.
- Gustafson, David L.
- Hansen, Nancy F.
- Horgan, Adrian M.
- Ivanov, Denis V.
- James, Terena
- Kang, Gyoung-Dong
- Kumar, Anil
- Lee, Sarah E.
- Luo, Shujun
- Martin, John W.
- Mehta, Parul
- Ning, Zemin
- O’Neill, Michael J.
- Rogers, John
- Romieu, Anthony
- Sanches-Kuiper, Raquel M.
- Shaw, Richard J.
- Smith, Melanie A.
- Turcatti, Gerardo
- Wang, Jingwen
- Yan, Juying
- Mullikin, James C.
- Hurles, Matthew E.
- Klenerman, David
- Durbin, Richard
- Venue
- Nature
- Published
- 2008-11
- Volume
- 456
- Issue
- 7218
- Pages
- 53-59
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2581791
- OpenAlex
- W2012016911
- Cited by
- 3,684
- References
- 36
- Citations by year
- 2026: 95 · 2025: 110 · 2024: 150 · 2023: 122 · 2022: 127 · 2021: 165 · 2020: 175 · 2019: 157 · 2018: 183 · 2017: 194 · 2016: 233 · 2015: 235 · 2014: 260 · 2013: 307 · 2012: 330
- FWCI
- 115.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DMU Open Research Archive (De Montfort University) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- Wellcome Trust
- National Institutes of Health
- Directorate for Biological Sciences
- Goddard Space Flight Center
- Biotechnology and Biological Sciences Research Council (B05823, MOL04534)
- National Human Genome Research Institute (Z01HG200330)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- whole-genome resequencing, single-molecule DNA sequencing, single nucleotide polymorphisms, structural variants, genetic ancestry, population genetic variation, X chromosome, consensus sequence, genome-wide association study
- MeSH terms
- Genotype, Humans, Male, Nigeria, Sensitivity and Specificity, Genome, Human, Consensus Sequence, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genomics, Chromosomes, Human, X
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
